data_5Y1E # _model_server_result.job_id '_vpbnWYMpB4pSLLy80EZow' _model_server_result.datetime_utc '2025-07-15 05:45:50' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 5y1e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 5Y1E # _exptl.entry_id 5Y1E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 663.425 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description NICOTINAMIDE-ADENINE-DINUCLEOTIDE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 105.6 _cell.angle_gamma 90 _cell.entry_id 5Y1E _cell.length_a 112.594 _cell.length_b 50.857 _cell.length_c 55.252 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y1E _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C21 H27 N7 O14 P2' _chem_comp.formula_weight 663.425 _chem_comp.id NAD _chem_comp.mon_nstd_flag . _chem_comp.name NICOTINAMIDE-ADENINE-DINUCLEOTIDE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag PA O1A NAD doub 237 n n PA O2A NAD sing 238 n n PA O5B NAD sing 239 n n PA O3 NAD sing 240 n n O2A HOA2 NAD sing 241 n n O5B C5B NAD sing 242 n n C5B C4B NAD sing 243 n n C5B H51A NAD sing 244 n n C5B H52A NAD sing 245 n n C4B O4B NAD sing 246 n n C4B C3B NAD sing 247 n n C4B H4B NAD sing 248 n n O4B C1B NAD sing 249 n n C3B O3B NAD sing 250 n n C3B C2B NAD sing 251 n n C3B H3B NAD sing 252 n n O3B HO3A NAD sing 253 n n C2B O2B NAD sing 254 n n C2B C1B NAD sing 255 n n C2B H2B NAD sing 256 n n O2B HO2A NAD sing 257 n n C1B N9A NAD sing 258 n n C1B H1B NAD sing 259 n n N9A C8A NAD sing 260 n y N9A C4A NAD sing 261 n y C8A N7A NAD doub 262 n y C8A H8A NAD sing 263 n n N7A C5A NAD sing 264 n y C5A C6A NAD sing 265 n y C5A C4A NAD doub 266 n y C6A N6A NAD sing 267 n n C6A N1A NAD doub 268 n y N6A H61A NAD sing 269 n n N6A H62A NAD sing 270 n n N1A C2A NAD sing 271 n y C2A N3A NAD doub 272 n y C2A H2A NAD sing 273 n n N3A C4A NAD sing 274 n y O3 PN NAD sing 275 n n PN O1N NAD doub 276 n n PN O2N NAD sing 277 n n PN O5D NAD sing 278 n n O5D C5D NAD sing 279 n n C5D C4D NAD sing 280 n n C5D H51N NAD sing 281 n n C5D H52N NAD sing 282 n n C4D O4D NAD sing 283 n n C4D C3D NAD sing 284 n n C4D H4D NAD sing 285 n n O4D C1D NAD sing 286 n n C3D O3D NAD sing 287 n n C3D C2D NAD sing 288 n n C3D H3D NAD sing 289 n n O3D HO3N NAD sing 290 n n C2D O2D NAD sing 291 n n C2D C1D NAD sing 292 n n C2D H2D NAD sing 293 n n O2D HO2N NAD sing 294 n n C1D N1N NAD sing 295 n n C1D H1D NAD sing 296 n n N1N C2N NAD sing 297 n y N1N C6N NAD doub 298 n y C2N C3N NAD doub 299 n y C2N H2N NAD sing 300 n n C3N C7N NAD sing 301 n n C3N C4N NAD sing 302 n y C7N O7N NAD doub 303 n n C7N N7N NAD sing 304 n n N7N H71N NAD sing 305 n n N7N H72N NAD sing 306 n n C4N C5N NAD doub 307 n y C4N H4N NAD sing 308 n n C5N C6N NAD sing 309 n y C5N H5N NAD sing 310 n n C6N H6N NAD sing 311 n n # _atom_sites.entry_id 5Y1E _atom_sites.fract_transf_matrix[1][1] 0.008881 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00248 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.019663 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.018791 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 NAD A 1 401 1 NAD NAD . C 3 SER A 1 402 1 SER SER . D 4 HOH A 1 501 108 HOH HOH . D 4 HOH A 2 502 3 HOH HOH . D 4 HOH A 3 503 139 HOH HOH . D 4 HOH A 4 504 23 HOH HOH . D 4 HOH A 5 505 10 HOH HOH . D 4 HOH A 6 506 25 HOH HOH . D 4 HOH A 7 507 112 HOH HOH . D 4 HOH A 8 508 89 HOH HOH . D 4 HOH A 9 509 20 HOH HOH . D 4 HOH A 10 510 117 HOH HOH . D 4 HOH A 11 511 38 HOH HOH . D 4 HOH A 12 512 87 HOH HOH . D 4 HOH A 13 513 39 HOH HOH . D 4 HOH A 14 514 119 HOH HOH . D 4 HOH A 15 515 84 HOH HOH . D 4 HOH A 16 516 97 HOH HOH . D 4 HOH A 17 517 77 HOH HOH . D 4 HOH A 18 518 153 HOH HOH . D 4 HOH A 19 519 144 HOH HOH . D 4 HOH A 20 520 46 HOH HOH . D 4 HOH A 21 521 74 HOH HOH . D 4 HOH A 22 522 45 HOH HOH . D 4 HOH A 23 523 116 HOH HOH . D 4 HOH A 24 524 15 HOH HOH . D 4 HOH A 25 525 68 HOH HOH . D 4 HOH A 26 526 174 HOH HOH . D 4 HOH A 27 527 173 HOH HOH . D 4 HOH A 28 528 66 HOH HOH . D 4 HOH A 29 529 5 HOH HOH . D 4 HOH A 30 530 48 HOH HOH . D 4 HOH A 31 531 59 HOH HOH . D 4 HOH A 32 532 37 HOH HOH . D 4 HOH A 33 533 64 HOH HOH . D 4 HOH A 34 534 47 HOH HOH . D 4 HOH A 35 535 22 HOH HOH . D 4 HOH A 36 536 1 HOH HOH . D 4 HOH A 37 537 80 HOH HOH . D 4 HOH A 38 538 33 HOH HOH . D 4 HOH A 39 539 21 HOH HOH . D 4 HOH A 40 540 125 HOH HOH . D 4 HOH A 41 541 113 HOH HOH . D 4 HOH A 42 542 118 HOH HOH . D 4 HOH A 43 543 2 HOH HOH . D 4 HOH A 44 544 3 HOH HOH . D 4 HOH A 45 545 115 HOH HOH . D 4 HOH A 46 546 24 HOH HOH . D 4 HOH A 47 547 172 HOH HOH . D 4 HOH A 48 548 8 HOH HOH . D 4 HOH A 49 549 128 HOH HOH . D 4 HOH A 50 550 109 HOH HOH . D 4 HOH A 51 551 88 HOH HOH . D 4 HOH A 52 552 78 HOH HOH . D 4 HOH A 53 553 49 HOH HOH . D 4 HOH A 54 554 74 HOH HOH . D 4 HOH A 55 555 60 HOH HOH . D 4 HOH A 56 556 42 HOH HOH . D 4 HOH A 57 557 91 HOH HOH . D 4 HOH A 58 558 129 HOH HOH . D 4 HOH A 59 559 90 HOH HOH . D 4 HOH A 60 560 11 HOH HOH . D 4 HOH A 61 561 31 HOH HOH . D 4 HOH A 62 562 130 HOH HOH . D 4 HOH A 63 563 146 HOH HOH . D 4 HOH A 64 564 148 HOH HOH . D 4 HOH A 65 565 147 HOH HOH . D 4 HOH A 66 566 17 HOH HOH . D 4 HOH A 67 567 75 HOH HOH . D 4 HOH A 68 568 56 HOH HOH . D 4 HOH A 69 569 92 HOH HOH . D 4 HOH A 70 570 20 HOH HOH . D 4 HOH A 71 571 29 HOH HOH . D 4 HOH A 72 572 14 HOH HOH . D 4 HOH A 73 573 18 HOH HOH . D 4 HOH A 74 574 58 HOH HOH . D 4 HOH A 75 575 93 HOH HOH . D 4 HOH A 76 576 40 HOH HOH . D 4 HOH A 77 577 106 HOH HOH . D 4 HOH A 78 578 14 HOH HOH . D 4 HOH A 79 579 51 HOH HOH . D 4 HOH A 80 580 127 HOH HOH . D 4 HOH A 81 581 163 HOH HOH . D 4 HOH A 82 582 4 HOH HOH . D 4 HOH A 83 583 142 HOH HOH . D 4 HOH A 84 584 107 HOH HOH . D 4 HOH A 85 585 176 HOH HOH . D 4 HOH A 86 586 19 HOH HOH . D 4 HOH A 87 587 32 HOH HOH . D 4 HOH A 88 588 65 HOH HOH . D 4 HOH A 89 589 24 HOH HOH . D 4 HOH A 90 590 101 HOH HOH . D 4 HOH A 91 591 55 HOH HOH . D 4 HOH A 92 592 122 HOH HOH . D 4 HOH A 93 593 34 HOH HOH . D 4 HOH A 94 594 86 HOH HOH . D 4 HOH A 95 595 13 HOH HOH . D 4 HOH A 96 596 63 HOH HOH . D 4 HOH A 97 597 6 HOH HOH . D 4 HOH A 98 598 100 HOH HOH . D 4 HOH A 99 599 138 HOH HOH . D 4 HOH A 100 600 83 HOH HOH . D 4 HOH A 101 601 53 HOH HOH . D 4 HOH A 102 602 102 HOH HOH . D 4 HOH A 103 603 18 HOH HOH . D 4 HOH A 104 604 10 HOH HOH . D 4 HOH A 105 605 25 HOH HOH . D 4 HOH A 106 606 124 HOH HOH . D 4 HOH A 107 607 50 HOH HOH . D 4 HOH A 108 608 94 HOH HOH . D 4 HOH A 109 609 16 HOH HOH . D 4 HOH A 110 610 26 HOH HOH . D 4 HOH A 111 611 111 HOH HOH . D 4 HOH A 112 612 110 HOH HOH . D 4 HOH A 113 613 79 HOH HOH . D 4 HOH A 114 614 26 HOH HOH . D 4 HOH A 115 615 135 HOH HOH . D 4 HOH A 116 616 67 HOH HOH . D 4 HOH A 117 617 44 HOH HOH . D 4 HOH A 118 618 36 HOH HOH . D 4 HOH A 119 619 27 HOH HOH . D 4 HOH A 120 620 126 HOH HOH . D 4 HOH A 121 621 73 HOH HOH . D 4 HOH A 122 622 54 HOH HOH . D 4 HOH A 123 623 41 HOH HOH . D 4 HOH A 124 624 82 HOH HOH . D 4 HOH A 125 625 72 HOH HOH . D 4 HOH A 126 626 12 HOH HOH . D 4 HOH A 127 627 31 HOH HOH . D 4 HOH A 128 628 9 HOH HOH . D 4 HOH A 129 629 61 HOH HOH . D 4 HOH A 130 630 52 HOH HOH . D 4 HOH A 131 631 28 HOH HOH . D 4 HOH A 132 632 7 HOH HOH . D 4 HOH A 133 633 179 HOH HOH . D 4 HOH A 134 634 95 HOH HOH . D 4 HOH A 135 635 62 HOH HOH . D 4 HOH A 136 636 21 HOH HOH . D 4 HOH A 137 637 79 HOH HOH . D 4 HOH A 138 638 134 HOH HOH . D 4 HOH A 139 639 103 HOH HOH . D 4 HOH A 140 640 70 HOH HOH . D 4 HOH A 141 641 5 HOH HOH . D 4 HOH A 142 642 149 HOH HOH . D 4 HOH A 143 643 115 HOH HOH . D 4 HOH A 144 644 30 HOH HOH . D 4 HOH A 145 645 28 HOH HOH . D 4 HOH A 146 646 141 HOH HOH . D 4 HOH A 147 647 98 HOH HOH . D 4 HOH A 148 648 85 HOH HOH . D 4 HOH A 149 649 99 HOH HOH . D 4 HOH A 150 650 35 HOH HOH . D 4 HOH A 151 651 69 HOH HOH . D 4 HOH A 152 652 76 HOH HOH . D 4 HOH A 153 653 181 HOH HOH . D 4 HOH A 154 654 123 HOH HOH . D 4 HOH A 155 655 159 HOH HOH . D 4 HOH A 156 656 81 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 P PA NAD . . . B 2 19.025 -5.343 20.116 1 13.03 ? PA NAD 401 A 1 HETATM 2 O O1A NAD . . . B 2 18.885 -6.808 19.855 1 11.14 ? O1A NAD 401 A 1 HETATM 3 O O2A NAD . . . B 2 20.29 -4.686 20.54 1 13.7 ? O2A NAD 401 A 1 HETATM 4 O O5B NAD . . . B 2 17.867 -4.919 21.132 1 15.87 ? O5B NAD 401 A 1 HETATM 5 C C5B NAD . . . B 2 16.576 -5.479 21.033 1 17.31 ? C5B NAD 401 A 1 HETATM 6 C C4B NAD . . . B 2 16.071 -5.701 22.451 1 15.59 ? C4B NAD 401 A 1 HETATM 7 O O4B NAD . . . B 2 14.839 -6.437 22.341 1 16.18 ? O4B NAD 401 A 1 HETATM 8 C C3B NAD . . . B 2 17.025 -6.513 23.357 1 17.45 ? C3B NAD 401 A 1 HETATM 9 O O3B NAD . . . B 2 17.403 -5.694 24.508 1 18.37 ? O3B NAD 401 A 1 HETATM 10 C C2B NAD . . . B 2 16.234 -7.73 23.78 1 18.13 ? C2B NAD 401 A 1 HETATM 11 O O2B NAD . . . B 2 16.36 -8.043 25.179 1 19.23 ? O2B NAD 401 A 1 HETATM 12 C C1B NAD . . . B 2 14.801 -7.308 23.482 1 17.68 ? C1B NAD 401 A 1 HETATM 13 N N9A NAD . . . B 2 13.952 -8.481 23.287 1 15.78 ? N9A NAD 401 A 1 HETATM 14 C C8A NAD . . . B 2 14.277 -9.618 22.616 1 16.19 ? C8A NAD 401 A 1 HETATM 15 N N7A NAD . . . B 2 13.25 -10.489 22.677 1 15.07 ? N7A NAD 401 A 1 HETATM 16 C C5A NAD . . . B 2 12.277 -9.9 23.436 1 15.07 ? C5A NAD 401 A 1 HETATM 17 C C6A NAD . . . B 2 10.945 -10.277 23.92 1 14.5 ? C6A NAD 401 A 1 HETATM 18 N N6A NAD . . . B 2 10.399 -11.49 23.611 1 16.25 ? N6A NAD 401 A 1 HETATM 19 N N1A NAD . . . B 2 10.286 -9.364 24.66 1 14.25 ? N1A NAD 401 A 1 HETATM 20 C C2A NAD . . . B 2 10.794 -8.17 24.986 1 14.02 ? C2A NAD 401 A 1 HETATM 21 N N3A NAD . . . B 2 12.002 -7.749 24.609 1 13.74 ? N3A NAD 401 A 1 HETATM 22 C C4A NAD . . . B 2 12.761 -8.588 23.834 1 14.72 ? C4A NAD 401 A 1 HETATM 23 O O3 NAD . . . B 2 18.545 -4.683 18.73 1 15.07 ? O3 NAD 401 A 1 HETATM 24 P PN NAD . . . B 2 18.772 -3.219 18.172 1 14.01 ? PN NAD 401 A 1 HETATM 25 O O1N NAD . . . B 2 19.931 -3.327 17.189 1 15.93 ? O1N NAD 401 A 1 HETATM 26 O O2N NAD . . . B 2 18.756 -2.16 19.279 1 12.88 ? O2N NAD 401 A 1 HETATM 27 O O5D NAD . . . B 2 17.527 -3.073 17.223 1 17.18 ? O5D NAD 401 A 1 HETATM 28 C C5D NAD . . . B 2 16.352 -2.394 17.635 1 19.21 ? C5D NAD 401 A 1 HETATM 29 C C4D NAD . . . B 2 15.392 -2.267 16.447 1 15.11 ? C4D NAD 401 A 1 HETATM 30 O O4D NAD . . . B 2 16.021 -1.622 15.323 1 15.81 ? O4D NAD 401 A 1 HETATM 31 C C3D NAD . . . B 2 14.91 -3.606 15.956 1 14.43 ? C3D NAD 401 A 1 HETATM 32 O O3D NAD . . . B 2 13.57 -3.525 15.458 1 12.43 ? O3D NAD 401 A 1 HETATM 33 C C2D NAD . . . B 2 15.825 -3.897 14.784 1 15.96 ? C2D NAD 401 A 1 HETATM 34 O O2D NAD . . . B 2 15.257 -4.826 13.88 1 17.12 ? O2D NAD 401 A 1 HETATM 35 C C1D NAD . . . B 2 16.016 -2.504 14.195 1 14.11 ? C1D NAD 401 A 1 HETATM 36 N N1N NAD . . . B 2 17.251 -2.398 13.399 1 13.71 ? N1N NAD 401 A 1 HETATM 37 C C2N NAD . . . B 2 18.462 -2.321 13.972 1 10.9 ? C2N NAD 401 A 1 HETATM 38 C C3N NAD . . . B 2 19.606 -2.174 13.234 1 12.87 ? C3N NAD 401 A 1 HETATM 39 C C7N NAD . . . B 2 20.968 -2.133 13.889 1 13.69 ? C7N NAD 401 A 1 HETATM 40 O O7N NAD . . . B 2 21.127 -2.05 15.112 1 15.73 ? O7N NAD 401 A 1 HETATM 41 N N7N NAD . . . B 2 22.019 -2.192 13.114 1 9.46 ? N7N NAD 401 A 1 HETATM 42 C C4N NAD . . . B 2 19.492 -2.137 11.839 1 12.79 ? C4N NAD 401 A 1 HETATM 43 C C5N NAD . . . B 2 18.24 -2.195 11.274 1 12.6 ? C5N NAD 401 A 1 HETATM 44 C C6N NAD . . . B 2 17.116 -2.324 12.072 1 12.51 ? C6N NAD 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 44 #